# Lorax “Speaks for the Trees”¶

lorax is a Flask-based web service that uses asynchronous queues (via RQ) to calculate and serve up multiple sequence alignments and phylogenetic trees. lorax uses pre-calculated Hidden-Markov Models (HMM) of protein families together with hmmalign to calculate multiple sequence alignments in either peptide or DNA space.

lorax calculates phylogenetic trees from either DNA or protein sequences by external processes in a computationally-intensive step that can take from minutes to days depending on the number of sequences and their sizes. Generally the computational time increases linearly with the average length of sequences and as the square of the number of input sequences. The tree-building software that lorax knows about are:

Tree Builder Description
FastTree FastTree is the fastest tree-builder and is the default tree-building algorithm.
RAxML RAxML is believed to be the more accurate tree-building algorithm, but at its fastest is probably 100x slower than FastTree. It is possible to use the RaxML EPA algorithm to do placement of test sequences on existing RaxML trees.

## Sections¶

See the following sections for details: